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Add 2d curvedata model #405

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73 changes: 73 additions & 0 deletions backend/proteins/admin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@

from fpbase.util import uncache_protein_page
from proteins.models import (
BleachCurve,
BleachMeasurement,
Camera,
Dye,
Expand All @@ -22,10 +23,12 @@
FluorState,
Light,
Lineage,
MaturationCurve,
Microscope,
OpticalConfig,
Organism,
OSERMeasurement,
PKACurve,
Protein,
ProteinCollection,
SnapGenePlasmid,
Expand Down Expand Up @@ -398,6 +401,7 @@ class BleachMeasurementAdmin(VersionAdmin):
model = BleachMeasurement
autocomplete_fields = ("state", "reference")
list_select_related = ("state", "state__protein")
search_fields = ("state__protein__name",)


@admin.register(State)
Expand Down Expand Up @@ -892,3 +896,72 @@ def get_form(self, request, obj=None, **kwargs):
qs = qs.exclude(id=obj.id)
form.base_fields["parent"].queryset = qs
return form


# ############ CURVE ADMINS ###############


class CurveAdmin(VersionAdmin):
"""Base admin for curve models."""

list_display = ("__str__", "status", "x_min", "x_max", "reference", "modified")
list_filter = ("status", "created", "modified")
autocomplete_fields = ("reference",)
readonly_fields = ("x_min", "x_max", "created", "modified")
fieldsets = [
(None, {"fields": ("status",)}),
("Data Range", {"fields": (("x_min", "x_max"),), "classes": ("collapse",)}),
(
"Provenance",
{"fields": ("reference", "source", "notes"), "classes": ("collapse",)},
),
(
"Metadata",
{
"fields": (("created", "created_by"), ("modified", "updated_by")),
"classes": ("collapse",),
},
),
]


@admin.register(PKACurve)
class PKACurveAdmin(CurveAdmin):
model = PKACurve
autocomplete_fields = (*CurveAdmin.autocomplete_fields, "state")
list_select_related = ("state", "state__protein", "reference")
search_fields = ("state__protein__name",)
fieldsets = [
(None, {"fields": ("state", "status")}),
*CurveAdmin.fieldsets[1:],
]


@admin.register(BleachCurve)
class BleachCurveAdmin(CurveAdmin):
model = BleachCurve
autocomplete_fields = (*CurveAdmin.autocomplete_fields, "bleach_measurement")
list_select_related = (
"bleach_measurement",
"bleach_measurement__state",
"bleach_measurement__state__protein",
"reference",
)
search_fields = ("bleach_measurement__state__protein__name",)
fieldsets = [
(None, {"fields": ("bleach_measurement", "status")}),
*CurveAdmin.fieldsets[1:],
]


@admin.register(MaturationCurve)
class MaturationCurveAdmin(CurveAdmin):
model = MaturationCurve
autocomplete_fields = (*CurveAdmin.autocomplete_fields, "state")
list_select_related = ("state", "state__protein", "reference")
search_fields = ("state__protein__name",)
list_display = (*CurveAdmin.list_display[:4], "temperature", *CurveAdmin.list_display[4:])
fieldsets = [
(None, {"fields": ("state", "status", "temperature")}),
*CurveAdmin.fieldsets[1:],
]
95 changes: 95 additions & 0 deletions backend/proteins/migrations/0061_curve_data_models.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,95 @@
# Generated by Django 5.2.8 on 2026-01-06 16:25

import django.db.models.deletion
import django.utils.timezone
import model_utils.fields
from django.conf import settings
from django.db import migrations, models


class Migration(migrations.Migration):

dependencies = [
('proteins', '0060_spectrum_optimized_storage'),
('references', '0009_curve_data_models'),
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
]

operations = [
migrations.CreateModel(
name='BleachCurve',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('status', model_utils.fields.StatusField(choices=[('approved', 'approved'), ('pending', 'pending'), ('rejected', 'rejected')], default='approved', max_length=100, no_check_for_status=True, verbose_name='status')),
('status_changed', model_utils.fields.MonitorField(default=django.utils.timezone.now, monitor='status', verbose_name='status changed')),
('x_values', models.BinaryField(help_text='X values as float32 binary array')),
('y_values', models.BinaryField(help_text='Y values as float32 binary array')),
('x_min', models.FloatField(blank=True, help_text='Minimum X value', null=True)),
('x_max', models.FloatField(blank=True, help_text='Maximum X value', null=True)),
('source', models.CharField(blank=True, help_text='Source of the curve data', max_length=128)),
('notes', models.TextField(blank=True, help_text='Additional notes or conditions')),
('bleach_measurement', models.ForeignKey(help_text='BleachMeasurement this curve belongs to', on_delete=django.db.models.deletion.CASCADE, related_name='curves', to='proteins.bleachmeasurement')),
('created_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(class)s_author', to=settings.AUTH_USER_MODEL)),
('reference', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(class)s_curves', to='references.reference')),
('updated_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(class)s_modifier', to=settings.AUTH_USER_MODEL)),
],
options={
'verbose_name': 'Bleach Curve',
'verbose_name_plural': 'Bleach Curves',
'indexes': [models.Index(fields=['bleach_measurement_id', 'status'], name='bleachcurve_meas_status_idx')],
},
),
migrations.CreateModel(
name='MaturationCurve',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('status', model_utils.fields.StatusField(choices=[('approved', 'approved'), ('pending', 'pending'), ('rejected', 'rejected')], default='approved', max_length=100, no_check_for_status=True, verbose_name='status')),
('status_changed', model_utils.fields.MonitorField(default=django.utils.timezone.now, monitor='status', verbose_name='status changed')),
('x_values', models.BinaryField(help_text='X values as float32 binary array')),
('y_values', models.BinaryField(help_text='Y values as float32 binary array')),
('x_min', models.FloatField(blank=True, help_text='Minimum X value', null=True)),
('x_max', models.FloatField(blank=True, help_text='Maximum X value', null=True)),
('source', models.CharField(blank=True, help_text='Source of the curve data', max_length=128)),
('notes', models.TextField(blank=True, help_text='Additional notes or conditions')),
('temperature', models.FloatField(blank=True, help_text='Temperature in °C during maturation measurement', null=True)),
('created_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(class)s_author', to=settings.AUTH_USER_MODEL)),
('reference', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(class)s_curves', to='references.reference')),
('state', models.ForeignKey(help_text='Protein state this curve belongs to', on_delete=django.db.models.deletion.CASCADE, related_name='maturation_curves', to='proteins.state')),
('updated_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(class)s_modifier', to=settings.AUTH_USER_MODEL)),
],
options={
'verbose_name': 'Maturation Curve',
'verbose_name_plural': 'Maturation Curves',
'indexes': [models.Index(fields=['state_id', 'status'], name='matcurve_state_status_idx')],
},
),
migrations.CreateModel(
name='PKACurve',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('status', model_utils.fields.StatusField(choices=[('approved', 'approved'), ('pending', 'pending'), ('rejected', 'rejected')], default='approved', max_length=100, no_check_for_status=True, verbose_name='status')),
('status_changed', model_utils.fields.MonitorField(default=django.utils.timezone.now, monitor='status', verbose_name='status changed')),
('x_values', models.BinaryField(help_text='X values as float32 binary array')),
('y_values', models.BinaryField(help_text='Y values as float32 binary array')),
('x_min', models.FloatField(blank=True, help_text='Minimum X value', null=True)),
('x_max', models.FloatField(blank=True, help_text='Maximum X value', null=True)),
('source', models.CharField(blank=True, help_text='Source of the curve data', max_length=128)),
('notes', models.TextField(blank=True, help_text='Additional notes or conditions')),
('created_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(class)s_author', to=settings.AUTH_USER_MODEL)),
('reference', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(class)s_curves', to='references.reference')),
('state', models.ForeignKey(help_text='Protein state this curve belongs to', on_delete=django.db.models.deletion.CASCADE, related_name='pka_curves', to='proteins.state')),
('updated_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(class)s_modifier', to=settings.AUTH_USER_MODEL)),
],
options={
'verbose_name': 'pKa Curve',
'verbose_name_plural': 'pKa Curves',
'indexes': [models.Index(fields=['state_id', 'status'], name='pkacurve_state_status_idx')],
},
),
]
4 changes: 4 additions & 0 deletions backend/proteins/models/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from proteins.models.bleach import BleachMeasurement
from proteins.models.collection import ProteinCollection
from proteins.models.curve import BleachCurve, MaturationCurve, PKACurve
from proteins.models.dye import Dye, DyeState
from proteins.models.efficiency import OcFluorEff
from proteins.models.excerpt import Excerpt
Expand All @@ -15,6 +16,7 @@
from proteins.models.transition import StateTransition

__all__ = [
"BleachCurve",
"BleachMeasurement",
"Camera",
"Dye",
Expand All @@ -26,11 +28,13 @@
"FluorescenceMeasurement",
"Light",
"Lineage",
"MaturationCurve",
"Microscope",
"OSERMeasurement",
"OcFluorEff",
"OpticalConfig",
"Organism",
"PKACurve",
"Protein",
"ProteinCollection",
"SnapGenePlasmid",
Expand Down
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